Matteo Comin

J. Comput. Biol., 2024

USTAR2: Fast and Succinct Representation of k-mer Sets Using De Bruijn Graphs.

[BibT_eX]

[DOI]

Enrico Rossignolo

Proceedings of the 17th International Joint Conference on Biomedical Engineering Systems and Technologies, 2024

2023

ClassGraph: Improving Metagenomic Read Classification with Overlap Graphs.

[BibT_eX]

[DOI]

Margherita Cavattoni

J. Comput. Biol., May, 2023

USTAR: Improved Compression of k-mer Sets with Counters Using de Bruijn Graphs.

[BibT_eX]

[DOI]

Enrico Rossignolo

Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

Efficient Hashing of Multiple Spaced Seeds with Application.

[BibT_eX]

[DOI]

Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies, 2023

2022

K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification.

[BibT_eX]

[DOI]

Davide Storato

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

SPRISS: approximating frequent <i>k</i>-mers by sampling reads, and applications.

[BibT_eX]

[DOI]

Bioinform., 2022

Efficient k-mer Indexing with Application to Mapping-free SNP Genotyping.

[BibT_eX]

[DOI]

Mattia Marcolin

Francesco Andreace

Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies, 2022

2021

Fast alignment of reads to a variation graph with application to SNP detection.

[BibT_eX]

[DOI]

Maurilio Monsu

J. Integr. Bioinform., 2021

Special Issue of the 1st International Applied Bioinformatics Conference (iABC'21).

[BibT_eX]

[DOI]

J. Integr. Bioinform., 2021

MetaProb 2: Metagenomic Reads Binning Based on Assembly Using Minimizers and K-Mers Statistics.

[BibT_eX]

[DOI]

Francesco Andreace

J. Comput. Biol., 2021

Comparison of microbiome samples: methods and computational challenges.

[BibT_eX]

[DOI]

Briefings Bioinform., 2021

Boosting Metagenomic Classification with Reads Overlap Graphs.

[BibT_eX]

[DOI]

Margherita Cavattoni

Proceedings of the Bioinformatics Research and Applications - 17th International Symposium, 2021

2020

Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k-mer Hashing.

[BibT_eX]

[DOI]

J. Comput. Biol., 2020

Improving Metagenomic Classification Using Discriminative k-mers from Sequencing Data.

[BibT_eX]

[DOI]

Davide Storato

Proceedings of the Bioinformatics Research and Applications - 16th International Symposium, 2020

MetaProb 2: Improving Unsupervised Metagenomic Binning with Efficient Reads Assembly Using Minimizers.

[BibT_eX]

[DOI]

Francesco Andreace

Proceedings of the Computational Advances in Bio and Medical Sciences, 2020

2019

Indexing k-mers in linear space for quality value compression.

[BibT_eX]

[DOI]

Yoshihiro Shibuya

J. Bioinform. Comput. Biol., 2019

Better quality score compression through sequence-based quality smoothing.

[BibT_eX]

[DOI]

Yoshihiro Shibuya

BMC Bioinform., 2019

MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage.

[BibT_eX]

[DOI]

Jia Qian

BMC Bioinform., 2019

2018

FSH: fast spaced seed hashing exploiting adjacent hashes.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2018

Data-Driven Smart Bike-Sharing System by Implementing Machine Learning Algorithms.

[BibT_eX]

[DOI]

Jia Qian

Livio Pianura

Proceedings of the Sixth International Conference on Enterprise Systems, 2018

2017

Metagenomic reads binning with spaced seeds.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2017

Fast Spaced Seed Hashing.

[BibT_eX]

[DOI]

Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

Binning metagenomic reads with probabilistic sequence signatures based on spaced seeds.

[BibT_eX]

[DOI]

Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2017

Fast and Sensitive Classification of Short Metagenomic Reads with SKraken.

[BibT_eX]

[DOI]

Jia Qian

Davide Marchiori

Proceedings of the Biomedical Engineering Systems and Technologies, 2017

SKraken: Fast and Sensitive Classification of Short Metagenomic Reads based on Filtering Uninformative k-mers.

[BibT_eX]

[DOI]

Davide Marchiori

Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2017), 2017

Assembly-Free Techniques for NGS Data.

[BibT_eX]

[DOI]

Proceedings of the Algorithms for Next-Generation Sequencing Data, Techniques, 2017

2016

On the comparison of regulatory sequences with multiple resolution Entropic Profiles.

[BibT_eX]

[DOI]

Morris Antonello

BMC Bioinform., 2016

MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures.

[BibT_eX]

[DOI]

Bioinform., 2016

Higher recall in metagenomic sequence classification exploiting Overlapping Reads.

[BibT_eX]

[DOI]

Proceedings of the 6th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2016

2015

Clustering of reads with alignment-free measures and quality values.

[BibT_eX]

[DOI]

Andrea Leoni

Algorithms Mol. Biol., 2015

Fast Alignment-free Comparison for Regulatory Sequences using Multiple Resolution Entropic Profiles.

[BibT_eX]

Morris Antonelli

Proceedings of the BIOINFORMATICS 2015, 2015

2014

Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2014

Fast Entropic Profiler: An InformationTheoretic Approach for the Discovery ofPatterns in Genomes.

[BibT_eX]

[DOI]

Morris Antonello

IEEE ACM Trans. Comput. Biol. Bioinform., 2014

Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes.

[BibT_eX]

[DOI]

Montse Farreras

J. Comput. Biol., 2014

Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns.

[BibT_eX]

[DOI]

BMC Bioinform., 2014

QCluster: Extending Alignment-Free Measures with Quality Values for Reads Clustering.

[BibT_eX]

[DOI]

Andrea Leoni

Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

2013

Ultrametric networks: a new tool for phylogenetic analysis.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2013

Filtering Degenerate Patterns with Application to Protein Sequence Analysis.

[BibT_eX]

[DOI]

Algorithms, 2013

Efficient parallel construction of suffix trees for genomes larger than main memory.

[BibT_eX]

[DOI]

Montse Farreras

Proceedings of the 20th European MPI Users's Group Meeting, 2013

Fast Computation of Entropic Profiles for the Detection of Conservation in Genomes.

[BibT_eX]

[DOI]

Morris Antonello

Proceedings of the Pattern Recognition in Bioinformatics, 2013

Reducing the Space of Degenerate Patterns in Protein Remote Homology Detection.

[BibT_eX]

[DOI]

Proceedings of the 24th International Workshop on Database and Expert Systems Applications, 2013

2012

Alignment-free phylogeny of whole genomes using underlying subwords.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2012

Whole-Genome Phylogeny by Virtue of Unic Subwords.

[BibT_eX]

[DOI]

Proceedings of the 23rd International Workshop on Database and Expert Systems Applications, 2012

2011

The Irredundant Class Method for Remote Homology Detection of Protein Sequences.

[BibT_eX]

[DOI]

J. Comput. Biol., 2011

2010

VARUN: Discovering Extensible Motifs under Saturation Constraints.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2010

Classification of protein sequences by means of irredundant patterns.

[BibT_eX]

[DOI]

BMC Bioinform., 2010

Remote Homology Detection of Protein Sequences.

[BibT_eX]

[DOI]

Proceedings of the Structure Discovery in Biology: Motifs, Networks & Phylogenies, 06.06., 2010

2009

Binding Balls: Fast Detection of Binding Sites Using a Property of Spherical Fourier Transform.

[BibT_eX]

[DOI]

Frank Dellaert

J. Comput. Biol., 2009

2008

Detection of subtle variations as consensus motifs.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2008

Mining Overrepresented 3D Patterns of Secondary Structures in proteins.

[BibT_eX]

[DOI]

Giuseppe Zanotti

J. Bioinform. Comput. Biol., 2008

2007

Algorithmic re-structuring and data replication for protein structure comparison on a GRID.

[BibT_eX]

[DOI]

Giovanni Ciriello

Future Gener. Comput. Syst., 2007

Subtle Motif Discovery for Detection of DNA Regulatory Sites.

[BibT_eX]

[DOI]

Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007

2006

Mining, compressing and classifying with extensible motifs.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2006

Application re-structuring and data management on a grid environment: a case study for bioinformatics.

[BibT_eX]

[DOI]

Giovanni Ciriello

Proceedings of the 20th International Parallel and Distributed Processing Symposium (IPDPS 2006), 2006

2005

Bridging Lossy and Lossless Compression by Motif Pattern Discovery.

[BibT_eX]

[DOI]

Electron. Notes Discret. Math., 2005

Conservative extraction of over-represented extensible motifs.

[BibT_eX]

[DOI]

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

Off-Line Compression by Extensible Motifs.

[BibT_eX]

[DOI]

Proceedings of the 2005 Data Compression Conference (DCC 2005), 2005

2004

Grid Deployment Of Bioinformatics Applications: A Case Study In Protein Similarity Determination.

[BibT_eX]

[DOI]

Carlo Ferrari

Parallel Process. Lett., 2004

PROuST: A Comparison Method of Three-Dimensional Structures of Proteins Using Indexing Techniques.

[BibT_eX]

[DOI]

Giuseppe Zanotti

J. Comput. Biol., 2004

Modelling a Protein Structure Comparison Application on the Grid Using PROTEUS.

[BibT_eX]

[DOI]

Proceedings of the Scientific Applications of Grid Computing, First International Workshop, 2004

Motifs in Ziv-Lempel-Welch Clef.

[BibT_eX]

[DOI]